Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

47 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Hepatocellular Carcinoma (HCC) biomarker discovery cohort for small RNA profiling

ABSTRACT: Patients with Hepatocellular Carcinoma (HCC) and without HCC used for small read cluster identification and small RNA profiling.

INSTRUMENT(S): Illumina HiSeq 2500, unspecified

ORGANISM(S): Homo sapiens

SUBMITTER: Bojan Losic

PROVIDER: E-MTAB-8528 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Expression profiling of PBMC from patients with hepatocellular carcinoma

Project description:Aberrant gene expression analysis between peripheral blood mononuclear cell (PBMC) samples from healthy individuals and patients with pancreatic carcinoma, gastric carcinoma and hepatocellular carcinoma (HCC) were identified using Affymetrix gene arrays. Peripheral blood mononuclear cell (PBMC) from healthy individuals, patients with pancreatic carcinoma, gastric carcinoma and HCC were isolated and total RNA was extracted for Affymetrix gene microarray analysis.

2013-08-03 | E-GEOD-49515 | biostudies-arrayexpress

LncRNA expression profile in the plasma of HCC patients

Project description:We conducted this experiment in order to investigate the different expression level of lncRNAs involved in HCC patients and the control samples. In addition, we detected the expression of lncRNA via the lncRNA microrray in the patients who undertaken the tumor resection

2015-11-01 | E-MTAB-2563 | biostudies-arrayexpress

Circulating Microvesicles and Exosomes in Small Cell Lung Cancer by Quantitative Proteomics

Project description:Early detection of small cell lung cancer crucially demands highly reliable markers. Growing evidence suggests that extracellular vesicles carry tumor cell-specific cargo suitable as protein markers in cancer. Therefore, we isolated plasma-derived exosomes from newly diagnosed small cell lung cancer patients and investigated proteome dynamics of these exosomes aiming at improving the detection of small cell lung cancer. A total of 1,016 proteins were initially identified. After data processing and statistical analysis, several proteins were found to be differentially expressed in comparing small cell lung cancer patients and healthy individuals, indicating that circulating exosomes may encompass specific proteins with potential diagnostic attributes for small cell lung cancer. Furthermore, our data may indicate a novel tumor-suppressing role of blood coagulation and involvement of complement activation in small cell lung cancer pathogenesis.

2022-04-04 | PXD028885 | Pride

Prostate Cancer (PRC) training cohort for small RNA characterization

Project description:RNA sequencing study on prostate cancer (PRC) cohort for small RNA characterization across biofluids, tissue types and isolation techniques.

2022-06-01 | E-MTAB-8529 | biostudies-arrayexpress

Combined Tissue-Fluid Proteomics to Unravel Phenotypic Variability in Amyotrophic Lateral Sclerosis

Project description:The lack of biomarkers for early diagnosis, clinical stratification and to monitor treatment response has hampered the development of new therapies for amyotrophic lateral sclerosis (ALS), a clinically heterogeneous neurodegenerative disorder with a variable site of disease initiation and rate of progression. To identify new biomarkers and therapeutic targets, two separate proteomic workflows were applied to study the immunological response and the plasma/brain proteome in phenotypic variants of ALS. Conventional multiplex (TMT) proteomic analysis of peripheral blood mononuclear cells (PBMCs) was performed alongside a recently introduced method to profile neuronal-derived proteins in plasma using brain tissue-enhanced isobaric tagging (TMTcalibrator). The combined proteomic analysis allowed the detection of regulated proteins linked to ALS pathogenesis (RNA-binding protein FUS, superoxide dismutase Cu-Zn and neurofilaments light polypeptide) alongside newly identified candidate biomarkers (myosin-9, fructose-bisphosphate aldolase and plectin). In line with the proteomic results, orthogonal immunodetection showed changes in neurofilaments and ApoE in bulbar versus limb onset fast progressing ALS. Functional analysis of significantly regulated features showed enrichment of pathways involved in regulation of the immune response, Rho family GTPases, semaphorin and integrin signalling. Our cross-phenotype investigation of PBMCs and plasma/brain proteins provides a more sensitive biomarker exploratory platform than conventional case-control studies in a single matrix. The reported regulated proteins may represent novel biomarker candidates and potentially druggable targets.

2020-07-30 | PXD020493 | Pride

Extracellular Vesicles from patients with Antibody-Mediated Rejection induce tubular senescence and endothelial to mesenchymal transition by regulating complement activation through horizontal transfer of miRNAs

Project description:Extracellular vesicles (EV) has been shown to deliver potential microRNA (miRNA) as cargo for specific target cells; effectively, the EV unique nature of the bilayer allows miRNA to be protected from degradation. We used microarray analysis to compare the miRNA profiles of EV isolated from acute antibody-mediated allograft rejection patients (AAMR) and chronic antibody-mediated allograft rejection (CAMR) compared to Tx Controls patients. By microarray miRNA profiling we detected 42 miRNAs downregulated and 34 miRNAs upregulated with FDR < 0.05 and Fold change >2. Principal Component analysis showed that these 76 miRNAs were able to distinguish AMR-derived EV from healthy TX patients. We also investigated whether differences in EV miRNA content could separate AAMR and CAMR patients. We found 9 miRNAs differentially expressed in the two AMR groups (eight downregulated and only one upregulated in AAMR compared to CAMR; effectively, these miRNAs could distinguish AAMR-derived EV from CAMR-derived EV. We then investigated the possible target genes of these miRNAs according to their expression, fold change and the p value; interestingly, several targets were associated to CDKN1A and CDKN2A genes regulation.

2021-09-10 | E-MTAB-10447 | biostudies-arrayexpress

Identification of novel and already known altered micoRNAs lead to a deeper understanding of the development of type 1 diabetes mellitus

Project description:Type 1 diabetes is a chronic autoimmune disease which results in inefficient regulation of glucose homeostasis and can lead to different vascular comorbidities through life. Next generation sequencing analysis was firstly performed to identify miRNAs that were differentially expressed between groups (20 patients vs. 10 controls). The aim of this study is to analyze the expression profile of circulating miRNAs in the plasma of adult patients with well-established type 1 diabetes and with no associated comorbidities, compared to healthy subjects, to identify miRNAs that are specific from diabetes pathology, and to assess pathways and biological processes related to the state of this disease.

2024-01-01 | E-MTAB-12641 | biostudies-arrayexpress

Circulating Microvesicles and Exosomes in Small Cell Lung Cancer by Quantitative Proteomics

Project description:Early detection of small cell lung cancer crucially demands highly reliable markers. Growing evidence suggests that extracellular vesicles carry tumor cell-specific cargo suitable as protein markers in cancer. Therefore, we isolated plasma-derived microvesicles from newly diagnosed small cell lung cancer patients and investigated proteome dynamics of these microvesicles aiming at improving the detection of small cell lung cancer. A total of 1,223 proteins were initially identified. After data processing and statistical analysis, several proteins were found to be differentially expressed in comparing small cell lung cancer patients and healthy individuals. Furthermore, our data may indicate involvement of complement activation, integrin-mediated signaling, cell adhesion- and migration, and blood coagulation in small cell lung cancer pathogenesis.

2022-04-04 | PXD028944 | Pride

A combined strategy of global gene expression analysis and multiplex PCR established a 13-member gene signature for the diagnosis of human hepatocellular carcinoma.

Project description:Aberrant gene expression between HCC tumor tissues, histologically normal adjacent liver tissues and peripheral blood mononuclear cell (PBMC) samples from healthy individuals and patients with pancreatic carcinoma, gastric carcinoma and HCC were identified using Affymetrix gene arrays. A 13-member HCC-specific gene signature was identified and validated via custom-designed quantitative multiplexed gene expression analysis using the GenomeLab GeXP Genetic Analysis System (GeXP). Peripheral blood mononuclear cell (PBMC) from healthy individuals, patients with pancreatic carcinoma, gastric carcinoma, and HCC were isolated and total RNA was extracted for Affymetrix gene microarray analysis.

2014-02-24 | E-GEOD-36076 | biostudies-arrayexpress

Tumour-associated antigenic peptides are present in the HLA class I ligandome of cancer cell line derived extracellular vesicles.

Project description:The recent success of monoclonal antibody checkpoint inhibitor therapies that enhance the ability of CD8+ T cells to detect cancer-related antigenic peptides has refocused the need to fully understand the repertoire of peptides being presented to the immune system. Whilst the peptide ligandome presented by cell surface HLA class I molecules on cancer cells has been studied extensively, the ligandome of extracellular vesicles remains poorly defined. Here we report the HLA class I ligandome of both cell surface and extracellular vesicles from eight breast cancer cell lines (MCF7, MDA-MB-231, MDA-MB-361, MDA-MB-415, MDA-MB-453, HCC 1806, HCC 1395, and HCC 1954), and additionally the melanoma cell line ESTDAB-056 and the multiple myeloma line RPMI 8226. Utilising HLA class I immunoisolation and mass spectrometry we detected a total of 6574 peptides from the cell surface and 2461 peptides from the extracellular vesicles of the cell lines studied. Within the extracellular vesicle HLA class I ligandome we identified 150 peptides derived from tumour associated antigenic proteins, of which 19 peptides have been shown to elicit T cell responses in previous studies. Our data thus confirms for the first time the presence of clinically relevant tumour-associated antigenic peptides in the HLA class I ligandome present on EV.

2022-04-01 | PXD025345 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data